MolNFT v1 · #39075 · protein
Crystal structure and allosteric regulation of the cytoplasmic escherichia COLI L-asparaginase I
2HIM · L-asparaginase 1: “Crystal structure and allosteric regulation of the cytoplasmic escherichia COLI L-asparaginase I”. X-ray diffraction, 2 ligands (ASN, ASP), 19 pockets (best druggability 0.84). MolNFT v1 #39075 on GenesisL1: 3D…
- PDB
- 2HIM
- Type
- protein
- Length
- 1,308 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase 1
- EC
- 3.5.1.1
- UniProt
- P0A962
- Ligands
- ASN, ASP
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase 1 (EC 3.5.1.1) | protein | 324 | 32% helix, 23% strand | P0A962 |
| B | L-asparaginase 1 (EC 3.5.1.1) | protein | 329 | 32% helix, 22% strand | P0A962 |
| C | L-asparaginase 1 (EC 3.5.1.1) | protein | 324 | 32% helix, 23% strand | P0A962 |
| D | L-asparaginase 1 (EC 3.5.1.1) | protein | 331 | 31% helix, 23% strand | P0A962 |
Ligands and binding sites
- ASN · Asparagine · ligand · 8 copies · chains A, C, B, D
- ASP · Aspartic acid · ligand · 4 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.84 | 0.96 | 54 | ASN, EDO |
| 2 | 220 | 0.82 | 0.96 | 39 | ASN, EDO |
| 3 | 307 | 0.78 | 0.89 | 48 | empty |
| 4 | 146 | 0.78 | 0.95 | 27 | empty |
| 5 | 562 | 0.72 | 0.80 | 68 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1775 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1761 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1168 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1141 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 215 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2HIM · Crystal Structure and Allosteric Regulation of the Cytoplasmic Escherichia coli… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A962 · AlphaFold monomer V2.0 prediction for L-asparaginase 1 (P0A962) · a predicted model of the same protein · chain C against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0A962
- Elsewhere: RCSB PDB 2HIM · PDBe 2HIM · UniProt P0A962
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.